HEADER HYDROLASE 22-JAN-08 2ZGJ TITLE CRYSTAL STRUCTURE OF D86N-GZMM COMPLEXED WITH ITS OPTIMAL SYNTHESIZED TITLE 2 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANZYME M; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MET-ASE, NATURAL KILLER CELL GRANULAR PROTEASE, HU-MET-1, COMPND 5 MET-1 SERINE PROTEASE; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SSGKVPLS; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GZMM, MET1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26B-D86N-GZMM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: PEPTIDE SYNTHESIS KEYWDS SERINE PROTEASE, SYNTHESIZED PEPTIDE, CYTOLYSIS, GLYCOPROTEIN, KEYWDS 2 HYDROLASE, SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR L.F.WU,L.WANG,G.Q.HUA,K.LIU,Y.J.ZHAI,F.SUN,Z.S.FAN REVDAT 4 10-NOV-21 2ZGJ 1 REMARK SEQADV REVDAT 3 13-JUL-11 2ZGJ 1 VERSN REVDAT 2 07-JUL-09 2ZGJ 1 JRNL REVDAT 1 27-JAN-09 2ZGJ 0 JRNL AUTH L.WU,L.WANG,G.HUA,K.LIU,X.YANG,Y.ZHAI,M.BARTLAM,F.SUN,Z.FAN JRNL TITL STRUCTURAL BASIS FOR PROTEOLYTIC SPECIFICITY OF THE HUMAN JRNL TITL 2 APOPTOSIS-INDUCING GRANZYME M JRNL REF J.IMMUNOL. V. 183 421 2009 JRNL REFN ISSN 0022-1767 JRNL PMID 19542453 JRNL DOI 10.4049/JIMMUNOL.0803088 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15700 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 832 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.39000 REMARK 3 B12 (A**2) : -0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.274 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.407 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.019 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.859 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; 7.625 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ;30.499 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ;18.111 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ;18.954 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; 0.124 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; 0.007 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; 0.246 ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; 0.314 ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; 0.160 ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; 0.207 ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; 0.167 ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; 0.944 ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; 1.533 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; 2.543 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; 3.714 ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2260 -13.1958 0.9326 REMARK 3 T TENSOR REMARK 3 T11: -0.1601 T22: -0.1725 REMARK 3 T33: -0.1277 T12: -0.0293 REMARK 3 T13: 0.0048 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.9474 L22: 3.1169 REMARK 3 L33: 2.9007 L12: 1.0202 REMARK 3 L13: -0.5635 L23: -1.5323 REMARK 3 S TENSOR REMARK 3 S11: 0.0925 S12: 0.0515 S13: 0.1435 REMARK 3 S21: -0.0477 S22: 0.0439 S23: 0.2251 REMARK 3 S31: -0.0691 S32: -0.1876 S33: -0.1363 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 8 REMARK 3 ORIGIN FOR THE GROUP (A): 28.7376 -23.9182 4.4917 REMARK 3 T TENSOR REMARK 3 T11: 0.0093 T22: -0.1320 REMARK 3 T33: 0.0278 T12: -0.1116 REMARK 3 T13: 0.1012 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 53.8486 L22: 11.3052 REMARK 3 L33: 29.2031 L12: -3.2314 REMARK 3 L13: 22.2551 L23: 13.5737 REMARK 3 S TENSOR REMARK 3 S11: 0.3880 S12: 0.6965 S13: -0.7252 REMARK 3 S21: 0.7447 S22: 0.2340 S23: 0.1821 REMARK 3 S31: -0.5700 S32: 1.8389 S33: -0.6220 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 244 REMARK 3 ORIGIN FOR THE GROUP (A): 26.4549 -4.6491 -5.8872 REMARK 3 T TENSOR REMARK 3 T11: 0.1233 T22: -0.0194 REMARK 3 T33: 0.0931 T12: -0.0498 REMARK 3 T13: -0.2378 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.2315 L22: 11.6442 REMARK 3 L33: 12.0230 L12: -3.7816 REMARK 3 L13: -0.7862 L23: 1.8108 REMARK 3 S TENSOR REMARK 3 S11: 0.4854 S12: 0.4853 S13: -0.0897 REMARK 3 S21: -0.7203 S22: -0.1082 S23: -0.8990 REMARK 3 S31: 0.8413 S32: -0.3297 S33: -0.3771 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000027943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16608 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2ZGC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE, 0.2M LI2SO4, 21% PEG3350, REMARK 280 PH8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.56300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.12600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.12600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.56300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 232 REMARK 465 LEU A 233 REMARK 465 GLU A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 SER B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 57 -57.71 -126.12 REMARK 500 ASP A 60 48.17 -77.82 REMARK 500 ASP A 93 54.41 -92.48 REMARK 500 SER A 99 -154.53 -124.15 REMARK 500 SER A 109 155.15 -49.65 REMARK 500 PHE A 156 -113.64 -99.19 REMARK 500 SER A 199 -65.58 -123.78 REMARK 500 SER A 201 -144.20 -151.72 REMARK 500 ARG A 230 -166.77 -127.80 REMARK 500 LEU B 7 27.20 -61.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 230 SER A 231 143.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 244 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZGC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE HUMAN GRANZYME M REMARK 900 RELATED ID: 2ZGH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE HUMAN GRANZYME M COMPLEXED WITH ITS REMARK 900 PRODUCT DBREF 2ZGJ A 1 232 UNP P51124 GRAM_HUMAN 26 257 DBREF 2ZGJ B 1 8 PDB 2ZGJ 2ZGJ 1 8 SEQADV 2ZGJ ASN A 86 UNP P51124 ASP 111 ENGINEERED MUTATION SEQADV 2ZGJ LEU A 233 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ GLU A 234 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 235 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 236 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 237 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 238 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 239 UNP P51124 EXPRESSION TAG SEQADV 2ZGJ HIS A 240 UNP P51124 EXPRESSION TAG SEQRES 1 A 240 ILE ILE GLY GLY ARG GLU VAL ILE PRO HIS SER ARG PRO SEQRES 2 A 240 TYR MET ALA SER LEU GLN ARG ASN GLY SER HIS LEU CYS SEQRES 3 A 240 GLY GLY VAL LEU VAL HIS PRO LYS TRP VAL LEU THR ALA SEQRES 4 A 240 ALA HIS CYS LEU ALA GLN ARG MET ALA GLN LEU ARG LEU SEQRES 5 A 240 VAL LEU GLY LEU HIS THR LEU ASP SER PRO GLY LEU THR SEQRES 6 A 240 PHE HIS ILE LYS ALA ALA ILE GLN HIS PRO ARG TYR LYS SEQRES 7 A 240 PRO VAL PRO ALA LEU GLU ASN ASN LEU ALA LEU LEU GLN SEQRES 8 A 240 LEU ASP GLY LYS VAL LYS PRO SER ARG THR ILE ARG PRO SEQRES 9 A 240 LEU ALA LEU PRO SER LYS ARG GLN VAL VAL ALA ALA GLY SEQRES 10 A 240 THR ARG CYS SER MET ALA GLY TRP GLY LEU THR HIS GLN SEQRES 11 A 240 GLY GLY ARG LEU SER ARG VAL LEU ARG GLU LEU ASP LEU SEQRES 12 A 240 GLN VAL LEU ASP THR ARG MET CYS ASN ASN SER ARG PHE SEQRES 13 A 240 TRP ASN GLY SER LEU SER PRO SER MET VAL CYS LEU ALA SEQRES 14 A 240 ALA ASP SER LYS ASP GLN ALA PRO CYS LYS GLY ASP SER SEQRES 15 A 240 GLY GLY PRO LEU VAL CYS GLY LYS GLY ARG VAL LEU ALA SEQRES 16 A 240 GLY VAL LEU SER PHE SER SER ARG VAL CYS THR ASP ILE SEQRES 17 A 240 PHE LYS PRO PRO VAL ALA THR ALA VAL ALA PRO TYR VAL SEQRES 18 A 240 SER TRP ILE ARG LYS VAL THR GLY ARG SER ALA LEU GLU SEQRES 19 A 240 HIS HIS HIS HIS HIS HIS SEQRES 1 B 8 SER SER GLY LYS VAL PRO LEU SER HET SO4 A 241 5 HET SO4 A 242 5 HET SO4 A 243 5 HET SO4 A 244 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *98(H2 O) HELIX 1 1 ALA A 39 ALA A 44 5 6 HELIX 2 2 ARG A 46 ALA A 48 5 3 HELIX 3 3 ASP A 147 ASN A 152 1 6 HELIX 4 4 TYR A 220 GLY A 229 1 10 SHEET 1 A 6 ARG A 5 GLU A 6 0 SHEET 2 A 6 ARG A 139 VAL A 145 -1 O GLU A 140 N ARG A 5 SHEET 3 A 6 ARG A 119 GLY A 124 -1 N CYS A 120 O LEU A 143 SHEET 4 A 6 PRO A 185 CYS A 188 -1 O VAL A 187 N SER A 121 SHEET 5 A 6 VAL A 193 SER A 201 -1 O GLY A 196 N LEU A 186 SHEET 6 A 6 VAL B 5 PRO B 6 -1 O VAL B 5 N SER A 201 SHEET 1 B 6 ARG A 5 GLU A 6 0 SHEET 2 B 6 ARG A 139 VAL A 145 -1 O GLU A 140 N ARG A 5 SHEET 3 B 6 MET A 165 ALA A 169 -1 O ALA A 169 N GLN A 144 SHEET 4 B 6 VAL A 213 ALA A 216 -1 O ALA A 214 N VAL A 166 SHEET 5 B 6 VAL A 193 SER A 201 -1 N VAL A 197 O THR A 215 SHEET 6 B 6 VAL B 5 PRO B 6 -1 O VAL B 5 N SER A 201 SHEET 1 C 7 LEU A 64 PHE A 66 0 SHEET 2 C 7 LEU A 50 LEU A 54 -1 N LEU A 52 O PHE A 66 SHEET 3 C 7 MET A 15 ARG A 20 -1 N GLN A 19 O ARG A 51 SHEET 4 C 7 SER A 23 HIS A 32 -1 O CYS A 26 N LEU A 18 SHEET 5 C 7 TRP A 35 THR A 38 -1 O LEU A 37 N VAL A 29 SHEET 6 C 7 ALA A 88 LEU A 92 -1 O LEU A 90 N VAL A 36 SHEET 7 C 7 ILE A 68 GLN A 73 -1 N ILE A 72 O LEU A 89 SSBOND 1 CYS A 26 CYS A 42 1555 1555 2.07 SSBOND 2 CYS A 120 CYS A 188 1555 1555 2.03 SSBOND 3 CYS A 151 CYS A 167 1555 1555 2.02 SSBOND 4 CYS A 178 CYS A 205 1555 1555 2.10 CISPEP 1 VAL A 80 PRO A 81 0 3.16 SITE 1 AC1 7 LYS A 34 GLN A 91 ARG A 203 VAL A 204 SITE 2 AC1 7 HOH A 257 HOH A 292 HOH A 302 SITE 1 AC2 2 ARG A 51 HIS A 67 SITE 1 AC3 3 GLY A 189 LYS A 190 HOH A 300 SITE 1 AC4 4 ARG A 46 MET A 47 ALA A 48 LYS A 173 CRYST1 74.487 74.487 112.689 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013425 0.007751 0.000000 0.00000 SCALE2 0.000000 0.015502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008874 0.00000